Improve usage

[nicholst]

Currently usage, introduced with this commit...

2801b7b

... omits mention of several input files in the inputs directory, i.e.

Z.txt
counts.txt
foci.txt
paper.txt

Further, there is no documentation on the files created in the outputs directory

alpha.txt
hmc.txt
gps/gp_*.txt
gp_summaries.txt
starting.txt
rfx.txt
burnin.txt

@yifan0330 - Can you pick this up?

[yifan0330]

okay! should I add their documentations in the manual?

[nicholst]

Sure, but for starters might as well put it in the usage. (What manual are you referring to?)

[yifan0330]

So I guess I should put it into usage in README.md? I should have pulled a request.

[nicholst]

I would put the information on the additional inputs and the outputs in the Usage printout in the code, and then copied the Usage print out into README.md (which is what I've done so far...do you see it in README.md?)

[yifan0330]

oh I am sorry, I only modified README.md previously.......now the Usage printout in main.cu should also be changed